Contacts of the strand formed by residues 211 - 215 (chain A) in PDB entry 3K0J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ASN* 3.0 15.1 + - - +
210A HIS* 1.3 82.7 - - - +
212A ILE* 1.3 72.1 + - - +
256A PHE* 3.8 23.3 - - + -
257A VAL 3.2 13.2 - - - +
258A ILE* 3.4 15.6 - - + +
286A TYR* 3.7 1.6 - - - -
287A ALA* 2.8 40.4 + - + +
289A THR 5.3 0.2 - - - -
291A SER* 2.9 27.6 + - - +
294A ILE* 4.8 1.0 - - - +
28E A 5.0 0.2 - - - -
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A HIS 4.0 0.2 + - - -
211A THR* 1.3 77.1 - - - +
213A TYR* 1.3 58.5 + - - +
214A ILE* 4.0 4.7 + - + +
234A PHE* 3.7 40.2 - - + -
256A PHE* 3.6 5.2 - - - -
257A VAL* 3.1 45.3 + - + +
259A PHE* 4.2 8.3 - - + -
265A ALA* 3.6 38.8 - - + +
268A ALA* 4.5 1.8 - - + -
269A LEU* 4.2 6.7 - - + -
284A ILE* 3.7 21.3 - - + -
285A GLN 3.3 6.1 - - - +
286A TYR* 4.7 4.5 - - + -
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 1.3 73.1 - - - +
214A ILE* 1.3 62.4 + - - +
215A ASN* 3.9 24.7 - - + -
254A GLN* 2.4 49.1 + - + +
255A ALA 3.8 4.7 - - - -
256A PHE* 3.7 26.2 - + + -
283A ARG 3.5 1.0 - - - +
284A ILE* 3.2 4.6 - - - -
285A GLN* 2.5 42.5 + - - +
287A ALA* 4.1 4.9 - - - +
26E G 3.3 11.6 + - - -
27E C 3.3 67.9 + + + +
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 4.1 7.6 - - + +
213A TYR* 1.3 78.1 - - - +
215A ASN* 1.3 65.1 + - - +
217A LEU* 3.6 25.6 - - + -
230A LEU* 4.5 10.5 - - + -
234A PHE* 3.3 35.4 - - + -
254A GLN* 3.2 5.5 - - - +
255A ALA* 3.0 38.7 + - + +
257A VAL* 3.8 21.5 - - + -
282A MET* 3.8 19.1 - - + -
283A ARG 3.1 11.9 - - - +
284A ILE* 4.1 14.6 - - + -
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Residues in contact with ASN 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TYR* 3.8 17.5 - - + +
214A ILE* 1.3 76.9 - - - +
216A ASN* 1.3 69.8 + - - +
217A LEU* 3.0 7.6 + - - -
253A GLY 3.5 7.6 - - - -
254A GLN* 4.0 2.0 - - + -
282A MET* 3.6 4.3 - - - +
283A ARG* 3.0 69.9 + - - +
285A GLN* 3.9 13.1 + - - +
25E U 4.1 5.0 + - - +
26E G 3.6 29.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il